null Sun 23 Dec 22:23:05 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2fzt-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fzt-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:15 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fzt-2.0-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.4860 Checking the provided sequence file Detected sequence length: 79 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 158 Adjusted target solvent content: 0.51 Input MTZ file: 2fzt-2.0-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 49.630 27.430 65.380 90.000 102.600 90.000 Input sequence file: 2fzt-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1264 target number of atoms Had to go as low as 0.55 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 1 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 63.805 2.000 Wilson plot Bfac: 20.33 11159 reflections ( 99.79 % complete ) and 0 restraints for refining 1403 atoms. Observations/parameters ratio is 1.99 ------------------------------------------------------ Starting model: R = 0.3570 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3031 (Rfree = 0.000) for 1403 atoms. Found 43 (48 requested) and removed 24 (24 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.01 1.98 NCS extension: 0 residues added, 1422 seeds are put forward Round 1: 101 peptides, 14 chains. Longest chain 12 peptides. Score 0.577 Round 2: 131 peptides, 10 chains. Longest chain 34 peptides. Score 0.822 Round 3: 143 peptides, 10 chains. Longest chain 27 peptides. Score 0.856 Round 4: 151 peptides, 5 chains. Longest chain 60 peptides. Score 0.927 Round 5: 152 peptides, 3 chains. Longest chain 76 peptides. Score 0.946 Taking the results from Round 5 Chains 5, Residues 149, Estimated correctness of the model 99.7 % 3 chains (147 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 51 B and 57 B 3 chains (153 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1420 restraints for refining 1464 atoms. 140 conditional restraints added. Observations/parameters ratio is 1.91 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3094 (Rfree = 0.000) for 1464 atoms. Found 50 (50 requested) and removed 32 (25 requested) atoms. Cycle 2: After refmac, R = 0.2841 (Rfree = 0.000) for 1471 atoms. Found 43 (49 requested) and removed 25 (25 requested) atoms. Cycle 3: After refmac, R = 0.2643 (Rfree = 0.000) for 1475 atoms. Found 35 (49 requested) and removed 25 (25 requested) atoms. Cycle 4: After refmac, R = 0.2502 (Rfree = 0.000) for 1479 atoms. Found 41 (47 requested) and removed 21 (25 requested) atoms. Cycle 5: After refmac, R = 0.2406 (Rfree = 0.000) for 1491 atoms. Found 17 (47 requested) and removed 25 (25 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1486 seeds are put forward Round 1: 154 peptides, 3 chains. Longest chain 76 peptides. Score 0.948 Round 2: 151 peptides, 4 chains. Longest chain 74 peptides. Score 0.936 Round 3: 151 peptides, 9 chains. Longest chain 30 peptides. Score 0.887 Round 4: 154 peptides, 3 chains. Longest chain 74 peptides. Score 0.948 Round 5: 153 peptides, 7 chains. Longest chain 41 peptides. Score 0.911 Taking the results from Round 4 Chains 3, Residues 151, Estimated correctness of the model 99.7 % 2 chains (131 residues) have been docked in sequence Building loops using Loopy2018 3 chains (151 residues) following loop building 2 chains (131 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1586 restraints for refining 1465 atoms. 397 conditional restraints added. Observations/parameters ratio is 1.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2601 (Rfree = 0.000) for 1465 atoms. Found 45 (45 requested) and removed 27 (25 requested) atoms. Cycle 7: After refmac, R = 0.2414 (Rfree = 0.000) for 1481 atoms. Found 26 (44 requested) and removed 19 (25 requested) atoms. Cycle 8: After refmac, R = 0.2320 (Rfree = 0.000) for 1488 atoms. Found 24 (43 requested) and removed 9 (25 requested) atoms. Cycle 9: After refmac, R = 0.2263 (Rfree = 0.000) for 1500 atoms. Found 25 (44 requested) and removed 10 (25 requested) atoms. Cycle 10: After refmac, R = 0.2195 (Rfree = 0.000) for 1515 atoms. Found 22 (44 requested) and removed 5 (25 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.93 1.90 NCS extension: 9 residues added (6 deleted due to clashes), 1544 seeds are put forward Round 1: 155 peptides, 2 chains. Longest chain 78 peptides. Score 0.957 Round 2: 154 peptides, 3 chains. Longest chain 78 peptides. Score 0.948 Round 3: 155 peptides, 4 chains. Longest chain 78 peptides. Score 0.941 Round 4: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 5: 153 peptides, 5 chains. Longest chain 50 peptides. Score 0.930 Taking the results from Round 1 Chains 2, Residues 153, Estimated correctness of the model 99.8 % 2 chains (153 residues) have been docked in sequence Building loops using Loopy2018 2 chains (153 residues) following loop building 2 chains (153 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1402 restraints for refining 1510 atoms. 117 conditional restraints added. Observations/parameters ratio is 1.85 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2305 (Rfree = 0.000) for 1510 atoms. Found 44 (44 requested) and removed 27 (25 requested) atoms. Cycle 12: After refmac, R = 0.2203 (Rfree = 0.000) for 1525 atoms. Found 35 (44 requested) and removed 19 (26 requested) atoms. Cycle 13: After refmac, R = 0.2121 (Rfree = 0.000) for 1539 atoms. Found 39 (43 requested) and removed 7 (26 requested) atoms. Cycle 14: After refmac, R = 0.2055 (Rfree = 0.000) for 1569 atoms. Found 34 (43 requested) and removed 17 (26 requested) atoms. Cycle 15: After refmac, R = 0.2033 (Rfree = 0.000) for 1584 atoms. Found 38 (44 requested) and removed 18 (27 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 1605 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 3: 156 peptides, 3 chains. Longest chain 78 peptides. Score 0.950 Round 4: 153 peptides, 5 chains. Longest chain 50 peptides. Score 0.930 Round 5: 149 peptides, 4 chains. Longest chain 56 peptides. Score 0.934 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1435 restraints for refining 1536 atoms. 158 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2208 (Rfree = 0.000) for 1536 atoms. Found 38 (43 requested) and removed 27 (26 requested) atoms. Cycle 17: After refmac, R = 0.2112 (Rfree = 0.000) for 1544 atoms. Found 28 (42 requested) and removed 12 (26 requested) atoms. Cycle 18: After refmac, R = 0.2060 (Rfree = 0.000) for 1559 atoms. Found 24 (42 requested) and removed 15 (26 requested) atoms. Cycle 19: After refmac, R = 0.2027 (Rfree = 0.000) for 1566 atoms. Found 35 (41 requested) and removed 10 (26 requested) atoms. Cycle 20: After refmac, R = 0.2005 (Rfree = 0.000) for 1589 atoms. Found 24 (42 requested) and removed 26 (27 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1588 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 157 peptides, 3 chains. Longest chain 78 peptides. Score 0.951 Round 3: 155 peptides, 4 chains. Longest chain 78 peptides. Score 0.941 Round 4: 153 peptides, 7 chains. Longest chain 32 peptides. Score 0.911 Round 5: 155 peptides, 4 chains. Longest chain 78 peptides. Score 0.941 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1433 restraints for refining 1533 atoms. 156 conditional restraints added. Observations/parameters ratio is 1.82 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2189 (Rfree = 0.000) for 1533 atoms. Found 40 (40 requested) and removed 28 (26 requested) atoms. Cycle 22: After refmac, R = 0.2116 (Rfree = 0.000) for 1541 atoms. Found 38 (38 requested) and removed 12 (26 requested) atoms. Cycle 23: After refmac, R = 0.2051 (Rfree = 0.000) for 1567 atoms. Found 35 (39 requested) and removed 13 (26 requested) atoms. Cycle 24: After refmac, R = 0.2006 (Rfree = 0.000) for 1589 atoms. Found 29 (40 requested) and removed 12 (27 requested) atoms. Cycle 25: After refmac, R = 0.1977 (Rfree = 0.000) for 1605 atoms. Found 34 (41 requested) and removed 17 (27 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1623 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 157 peptides, 4 chains. Longest chain 78 peptides. Score 0.943 Round 3: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 4: 150 peptides, 5 chains. Longest chain 56 peptides. Score 0.926 Round 5: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1455 restraints for refining 1559 atoms. 178 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2131 (Rfree = 0.000) for 1559 atoms. Found 39 (39 requested) and removed 28 (26 requested) atoms. Cycle 27: After refmac, R = 0.2069 (Rfree = 0.000) for 1569 atoms. Found 35 (38 requested) and removed 13 (26 requested) atoms. Cycle 28: After refmac, R = 0.2022 (Rfree = 0.000) for 1590 atoms. Found 30 (39 requested) and removed 10 (27 requested) atoms. Cycle 29: After refmac, R = 0.2007 (Rfree = 0.000) for 1609 atoms. Found 30 (40 requested) and removed 17 (27 requested) atoms. Cycle 30: After refmac, R = 0.1981 (Rfree = 0.000) for 1621 atoms. Found 27 (38 requested) and removed 19 (27 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1629 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 3: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Round 4: 152 peptides, 6 chains. Longest chain 48 peptides. Score 0.919 Round 5: 153 peptides, 5 chains. Longest chain 78 peptides. Score 0.930 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1445 restraints for refining 1571 atoms. 168 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2129 (Rfree = 0.000) for 1571 atoms. Found 36 (36 requested) and removed 26 (26 requested) atoms. Cycle 32: After refmac, R = 0.2042 (Rfree = 0.000) for 1579 atoms. Found 36 (36 requested) and removed 8 (27 requested) atoms. Cycle 33: After refmac, R = 0.2008 (Rfree = 0.000) for 1605 atoms. Found 24 (36 requested) and removed 16 (27 requested) atoms. Cycle 34: After refmac, R = 0.1963 (Rfree = 0.000) for 1611 atoms. Found 30 (35 requested) and removed 14 (27 requested) atoms. Cycle 35: After refmac, R = 0.1973 (Rfree = 0.000) for 1625 atoms. Found 30 (35 requested) and removed 27 (27 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.93 1.90 NCS extension: 0 residues added, 1628 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 154 peptides, 4 chains. Longest chain 78 peptides. Score 0.940 Round 3: 151 peptides, 5 chains. Longest chain 78 peptides. Score 0.927 Round 4: 152 peptides, 6 chains. Longest chain 78 peptides. Score 0.919 Round 5: 151 peptides, 5 chains. Longest chain 68 peptides. Score 0.927 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1466 restraints for refining 1571 atoms. 189 conditional restraints added. Observations/parameters ratio is 1.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2086 (Rfree = 0.000) for 1571 atoms. Found 33 (33 requested) and removed 27 (26 requested) atoms. Cycle 37: After refmac, R = 0.2012 (Rfree = 0.000) for 1575 atoms. Found 30 (32 requested) and removed 11 (27 requested) atoms. Cycle 38: After refmac, R = 0.1986 (Rfree = 0.000) for 1590 atoms. Found 27 (32 requested) and removed 16 (27 requested) atoms. Cycle 39: After refmac, R = 0.1948 (Rfree = 0.000) for 1601 atoms. Found 22 (31 requested) and removed 10 (27 requested) atoms. Cycle 40: After refmac, R = 0.1949 (Rfree = 0.000) for 1612 atoms. Found 27 (32 requested) and removed 11 (27 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 1628 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 152 peptides, 3 chains. Longest chain 78 peptides. Score 0.946 Round 3: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 4: 150 peptides, 4 chains. Longest chain 78 peptides. Score 0.935 Round 5: 153 peptides, 5 chains. Longest chain 55 peptides. Score 0.930 Taking the results from Round 1 Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ 11159 reflections ( 99.79 % complete ) and 1446 restraints for refining 1557 atoms. 169 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2128 (Rfree = 0.000) for 1557 atoms. Found 31 (31 requested) and removed 27 (26 requested) atoms. Cycle 42: After refmac, R = 0.2036 (Rfree = 0.000) for 1560 atoms. Found 30 (30 requested) and removed 9 (26 requested) atoms. Cycle 43: After refmac, R = 0.1990 (Rfree = 0.000) for 1580 atoms. Found 25 (30 requested) and removed 18 (27 requested) atoms. Cycle 44: After refmac, R = 0.1964 (Rfree = 0.000) for 1586 atoms. Found 29 (29 requested) and removed 9 (27 requested) atoms. Cycle 45: After refmac, R = 0.1929 (Rfree = 0.000) for 1606 atoms. Found 30 (30 requested) and removed 22 (27 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.92 1.89 NCS extension: 0 residues added, 1614 seeds are put forward Round 1: 154 peptides, 2 chains. Longest chain 78 peptides. Score 0.956 Round 2: 151 peptides, 3 chains. Longest chain 78 peptides. Score 0.945 Round 3: 155 peptides, 3 chains. Longest chain 78 peptides. Score 0.949 Round 4: 142 peptides, 6 chains. Longest chain 78 peptides. Score 0.903 Round 5: 155 peptides, 4 chains. Longest chain 55 peptides. Score 0.941 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 2, Residues 152, Estimated correctness of the model 99.8 % 2 chains (152 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 2 chains (152 residues) following loop building 2 chains (152 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 11159 reflections ( 99.79 % complete ) and 1277 restraints for refining 1273 atoms. Observations/parameters ratio is 2.19 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2729 (Rfree = 0.000) for 1273 atoms. Found 14 (22 requested) and removed 0 (22 requested) atoms. Cycle 47: After refmac, R = 0.2603 (Rfree = 0.000) for 1273 atoms. Found 8 (23 requested) and removed 0 (22 requested) atoms. Cycle 48: After refmac, R = 0.2524 (Rfree = 0.000) for 1273 atoms. Found 2 (23 requested) and removed 1 (22 requested) atoms. Cycle 49: After refmac, R = 0.2477 (Rfree = 0.000) for 1273 atoms. Found 3 (23 requested) and removed 1 (22 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:53:42 GMT 2018 Job finished. TimeTaking 30.62 Used memory is bytes: 21587912